Complex Sampling Design

Published

Sunday, 21/01/2024

1 Practical

1.1 Setup Project

  1. Open your RStudio

  2. Create Project

  • File -> New Project…
  • New Directory -> New Project
    • set Directory Name, e.g., Sesi 4 NHMS
    • ensure the project directory is in default working directory, i.e., ~/Documents/RStudio
    • click Create Project button
  1. Copy your NHMS dataset into the working directory
  • Files pane -> click the ⚙️ More 🔻 button -> select Show Folder in New Window
  • Copy your NHMS dataset into the working directory
  • alternatively, you can also check you working directory, and copy the working directory into your File Explorer
Code 
getwd() %>% 
  clipr::write_clip()

2 Analysis

2.1 Import Dataset

SPSS sav file - Click the spss’s sav file - Select Import Dataset... - Copy the code into r code chunk - add function as_factor(_) - Note: as_factor (from haven package), - NOT as.factor (from base package)

Code 
```{r}
library(tidyverse)
library(haven)

nhms19ds <- read_sav("nhms19ds.sav") %>% 
  as_factor()

nhms19ds
```

Occasionally, you may have the original dataset in csv/xlsx file - similar step with SPSS - click the excel xlsx file - select import dataset - copy the code into r code chunk - appropriate data wrangling - label - recode - rename - relevel

Code 
```{r}
library(readxl)

xlsxnhms19 <- read_excel("NHMS_2019_CholData.xlsx")

xlsxnhms19
```
Code 
```{r}
library(haven)
library(labelled)
library(stringi)

xlsxnhms19_w <- xlsxnhms19 %>% 
  mutate(INDVID = stri_sub(indvid, 2)) %>% 
  set_value_labels(c01 = c("EJ" = -9, "TT" = -7, "N/A" = -6, 
                           "Yes" = 1, "No" = 2), 
                   c02 = c("EJ" = -9, "TT" = -7, "N/A" = -6, 
                           "Yes" = 1, "No" = 2), 
                   c03 = c("TT" = -7, "N/A" = -6, 
                           "Less than 1 year" = 1, "1 year and more" = 2), 
                   c03a = c("TT" = -7, "N/A" = -6), 
                   c04a = c("N/A" = -6, "Yes" = 1, "No" = 2), 
                   c04b = c("TT" = -7, "N/A" = -6, "Yes" = 1, "No" = 2), 
                   c04c = c("TT" = -7, "N/A" = -6, "Yes" = 1, "No" = 2), 
                   c04d = c("TT" = -7, "N/A" = -6, "Yes" = 1, "No" = 2), 
                   c05 = c("TT" = -7, "N/A" = -6, "Yes" = 1, "No" = 2), 
                   c06 = c("EJ" = -9, "TT" = -7, "N/A" = -6, 
                           "Government clinic" = 1, "Private clinic" = 2,
                           "Government hospital" = 3, "Private hospital" = 4,
                           "Pharmacy (self-medicating)" = 5, 
                           "Traditional, herbal, complementary" = 6,
                           "Didn't seek treatment" = 7),
                   u303 = c("EJ" = -9, "N/A" = -6),
                   known_chol = c("N/A" = -6, "No" = 0, "Yes" = 1),
                   undiagnosed_chol = c("N/A" = -6, "No" = 0, "Yes" = 1),
                   total_chol = c("N/A" = -6, "No" = 0, "Yes" = 1),
                   bodyweight1 = c("EJ" = -9, "TB" = -8, "N/A" = -6),
                   bodyweight2 = c("EJ" = -9, "TB" = -8, "N/A" = -6),
                   bodyheight1 = c("EJ" = -9, "TB" = -8, "N/A" = -6), 
                   bodyheight2 = c("EJ" = -9, "TB" = -8, "N/A" = -6), 
                   wc1 = c("EJ" = -9, "TB" = -8, "N/A" = -6), 
                   wc2 = c("EJ" = -9, "TB" = -8, "N/A" = -6), 
                   weight = c("N/A" = -6), 
                   height = c("N/A" = -6), 
                   wc = c("N/A" = -6)) %>% 
  set_na_values(c01 = c(-9, -7, -6), 
                c02 = c(-9, -7, -6), 
                c03 = c(-7, -6), 
                c03a = c(-7, -6), 
                c04a = -6, 
                c04b = c(-7, -6), 
                c04c = c(-7, -6), 
                c04d = c(-7, -6), 
                c05 = c(-7, -6), 
                c06 = c(-9, -7, -6), 
                u303 = c(-9, -6), 
                known_chol = -6, 
                undiagnosed_chol = -6, 
                total_chol = -6, 
                bodyweight1 = c(-9, -8, -6), 
                bodyweight2 = c(-9, -8, -6), 
                bodyheight1 = c(-9, -8, -6), 
                bodyheight2 = c(-9, -8, -6), 
                wc1 = c(-9, -8, -6), 
                wc2 = c(-9, -8, -6), 
                weight = -6, 
                height = -6, 
                wc = -6) %>% 
  set_variable_labels(state_st = "PSU",
                      ebid = "EB ID - Cluster",
                      wtfinal_ncd = "Sampling Weight",
                      c01 = "ever had total blood cholesterol level measured",
                      c02 = "ever told have high cholesterol level", 
                      c03 = "when told to have high cholesterol", 
                      c03a = "years since was told to have high cholesterol", 
                      c04a = "on medication for past 2 week", 
                      c04b = "advice for special low fat diet", 
                      c04c = "advice to loose weight", 
                      c04d = "advice to exercise", 
                      c05 = "treatment - herbal/TCM", 
                      c06 = "common place to receive treatment",
                      u303 = "Total Cholesterol (mmol/L)",
                      bodyweight1 = "Body Weight (kg)",
                      bodyweight2 = "Body Weight (kg)",
                      weight = "Body Weight (kg)",
                      bodyheight1 = "Body Height (cm)",
                      bodyheight2 = "Body Height (cm)",
                      height = "Body Height (cm)",
                      wc1 = "Waist Circumference (cm)",
                      wc2 = "Waist Circumference (cm)",
                      wc = "Waist Circumference (cm)") %>% 
  to_factor(drop_unused_labels = T, user_na_to_na = T)

xlsxnhms19_w
```